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<a href="Bio-module.html">Package Bio</a> ::
Module Decode
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<h1 class="epydoc">Source Code for <a href="Bio.Decode-module.html">Module Bio.Decode</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Decode elements from a Std/Martel parsed XML stream</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Parsers=Bio.Parsers-module.html"><a title="Bio.Parsers" class="py-name" href="#" onclick="return doclink('link-1', 'Parsers', 'link-1');">Parsers</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.Parsers.spark=Bio.Parsers.spark-module.html"><a title="Bio.Parsers.spark" class="py-name" href="#" onclick="return doclink('link-2', 'spark', 'link-2');">spark</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Parsers.spark.GenericScanner=Bio.Parsers.spark.GenericScanner-class.html"><a title="Bio.Parsers.spark.GenericScanner" class="py-name" href="#" onclick="return doclink('link-3', 'GenericScanner', 'link-3');">GenericScanner</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.Parsers.spark.GenericParser=Bio.Parsers.spark.GenericParser-class.html"><a title="Bio.Parsers.spark.GenericParser" class="py-name" href="#" onclick="return doclink('link-4', 'GenericParser', 'link-4');">GenericParser</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="unescape_C"></a><div id="unescape_C-def"><a name="L6"></a><tt class="py-lineno"> 6</tt> <a class="py-toggle" href="#" id="unescape_C-toggle" onclick="return toggle('unescape_C');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#unescape_C">unescape_C</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="unescape_C-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="unescape_C-expanded"><a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-5" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-5', 'i', 'link-5');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-6', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-7" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-7', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt id="link-8" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-8', 'i', 'link-5');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">"\\"</tt><tt class="py-op">:</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-9', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-10', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt id="link-11" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-11', 'i', 'link-5');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-12', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt id="link-13" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-13', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt id="link-14" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-14', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-string">"x"</tt><tt class="py-op">:</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt id="link-15" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-15', 'x', 'link-15');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-16', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt id="link-17" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-17', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt id="link-18" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-18', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-19', 'x', 'link-15');">x</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"invalid \\x escape"</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-20', 'i', 'link-5');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-22', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">chr</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-5');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-string">"01234567"</tt><tt class="py-op">:</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-24', 'x', 'link-15');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-25', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt id="link-26" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-26', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-comment"># \octals don't do a length assertion check</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-5');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-29', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-30', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">chr</tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-31', 'i', 'link-5');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">result</tt><tt class="py-op">)</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="join_english"></a><div id="join_english-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="join_english-toggle" onclick="return toggle('join_english');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#join_english">join_english</a><tt class="py-op">(</tt><tt class="py-param">fields</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="join_english-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="join_english-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">fields</tt><tt class="py-op">:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">""</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-33', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">field</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-34" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-34', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"-"</tt> <tt class="py-keyword">and</tt> <tt id="link-35" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-35', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"-"</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt id="link-36" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-36', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-37', 's', 'link-6');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">field</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-38" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-38', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-39', 'find', 'link-39');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">field</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-40', 'find', 'link-39');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-41', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-42', 's', 'link-6');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-name">field</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-43', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-44', 's', 'link-6');">s</a></tt> <tt class="py-op">+</tt> <tt class="py-string">" "</tt> <tt class="py-op">+</tt> <tt class="py-name">field</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-45', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-46', 'split', 'link-46');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-47', 'strip', 'link-47');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="chomp"></a><div id="chomp-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="chomp-toggle" onclick="return toggle('chomp');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#chomp">chomp</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">c</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="chomp-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="chomp-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-48" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-48', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-49" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-49', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-50" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-50', 's', 'link-6');">s</a></tt> </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
<a name="lchomp"></a><div id="lchomp-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="lchomp-toggle" onclick="return toggle('lchomp');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#lchomp">lchomp</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">c</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="lchomp-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="lchomp-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-51" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-51', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-52" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-52', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-53" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-53', 's', 'link-6');">s</a></tt> </tt>
</div><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
<a name="chompchomp"></a><div id="chompchomp-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="chompchomp-toggle" onclick="return toggle('chompchomp');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#chompchomp">chompchomp</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">c</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="chompchomp-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="chompchomp-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-54" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-54', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">c</tt> <tt class="py-keyword">and</tt> <tt id="link-55" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-55', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-56" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-56', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-57" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-57', 's', 'link-6');">s</a></tt> </tt>
</div><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="fixspaces"></a><div id="fixspaces-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="fixspaces-toggle" onclick="return toggle('fixspaces');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#fixspaces">fixspaces</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="fixspaces-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="fixspaces-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-comment"># s.split breaks down to a list of words</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># " ".join puts them together</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># strip removes leading and trailing spaces</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-58', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-59', 'split', 'link-46');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-60', 'strip', 'link-47');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="join_fixspaces"></a><div id="join_fixspaces-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="join_fixspaces-toggle" onclick="return toggle('join_fixspaces');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#join_fixspaces">join_fixspaces</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="join_fixspaces-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="join_fixspaces-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-61', 'split', 'link-46');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-62', 'strip', 'link-47');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="tr"></a><div id="tr-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="tr-toggle" onclick="return toggle('tr');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#tr">tr</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">frm</tt><tt class="py-op">,</tt> <tt class="py-param">to</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="tr-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="tr-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt id="link-63" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-63', 'table', 'link-63');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">maketrans</tt><tt class="py-op">(</tt><tt class="py-name">frm</tt><tt class="py-op">,</tt> <tt class="py-name">to</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.GFF.Feature.translate()=Bio.GFF.Feature-class.html#translate,Method Bio.GFF.FeatureAggregate.translate()=Bio.GFF.FeatureAggregate-class.html#translate,Function Bio.Seq.translate()=Bio.Seq-module.html#translate,Function Bio.SeqUtils.translate()=Bio.SeqUtils-module.html#translate,Method Bio.Translate.Translator.translate()=Bio.Translate.Translator-class.html#translate,Function Bio.utils.translate()=Bio.utils-module.html#translate"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-64', 'translate', 'link-64');">translate</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-65', 's', 'link-6');">s</a></tt><tt class="py-op">,</tt> <tt id="link-66" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-66', 'table', 'link-63');">table</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="safe_int"></a><div id="safe_int-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="safe_int-toggle" onclick="return toggle('safe_int');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#safe_int">safe_int</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="safe_int-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="safe_int-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-docstring">"""converts to int if the number is small, long if it's large"""</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-67', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">long</tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-68', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt id="link-69" class="py-name" targets="Variable Bio.Decode.decode_functions=Bio.Decode-module.html#decode_functions"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-69', 'decode_functions', 'link-69');">decode_functions</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-string">"chomp"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-70" class="py-name" targets="Function Bio.Decode.chomp()=Bio.Decode-module.html#chomp"><a title="Bio.Decode.chomp" class="py-name" href="#" onclick="return doclink('link-70', 'chomp', 'link-70');">chomp</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-string">"chompchomp"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-71" class="py-name" targets="Function Bio.Decode.chompchomp()=Bio.Decode-module.html#chompchomp"><a title="Bio.Decode.chompchomp" class="py-name" href="#" onclick="return doclink('link-71', 'chompchomp', 'link-71');">chompchomp</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-string">"chop"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-72" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-72', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-73" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-73', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-string">"chopchop"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-74" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-74', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-75" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-75', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-string">"fixspaces"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-76" class="py-name" targets="Function Bio.Decode.fixspaces()=Bio.Decode-module.html#fixspaces"><a title="Bio.Decode.fixspaces" class="py-name" href="#" onclick="return doclink('link-76', 'fixspaces', 'link-76');">fixspaces</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-string">"lchomp"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-77" class="py-name" targets="Function Bio.Decode.lchomp()=Bio.Decode-module.html#lchomp"><a title="Bio.Decode.lchomp" class="py-name" href="#" onclick="return doclink('link-77', 'lchomp', 'link-77');">lchomp</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-string">"lchop"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-78" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-78', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-79" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-79', 's', 'link-6');">s</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-string">"lower"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-80" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-80', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-81" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-81', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-string">"lstrip"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-82" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-82', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-83" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-83', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">lstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-string">"replace"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-84" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-84', 's', 'link-6');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">old</tt><tt class="py-op">,</tt> <tt class="py-name">new</tt><tt class="py-op">:</tt> <tt id="link-85" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-85', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-name">old</tt><tt class="py-op">,</tt> <tt class="py-name">new</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-string">"rstrip"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-86" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-86', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-87" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-87', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-string">"str"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-string">"strip"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-88" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-88', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-89" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-89', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-90', 'strip', 'link-47');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-string">"tr"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-91" class="py-name" targets="Function Bio.Decode.tr()=Bio.Decode-module.html#tr"><a title="Bio.Decode.tr" class="py-name" href="#" onclick="return doclink('link-91', 'tr', 'link-91');">tr</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-string">"unescape.c"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-92" class="py-name" targets="Function Bio.Decode.unescape_C()=Bio.Decode-module.html#unescape_C"><a title="Bio.Decode.unescape_C" class="py-name" href="#" onclick="return doclink('link-92', 'unescape_C', 'link-92');">unescape_C</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-string">"unescape.doublequote"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-93" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-93', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-94" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-94', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'""'</tt><tt class="py-op">,</tt> <tt class="py-string">'"'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-string">"unescape.singlequote"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-95" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-95', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-96" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-96', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"''"</tt><tt class="py-op">,</tt> <tt class="py-string">"'"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-string">"upper"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-97" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-97', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-98" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-98', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-comment"># List operations</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-string">"join"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">lst</tt><tt class="py-op">,</tt> <tt id="link-99" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-99', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">:</tt> <tt id="link-100" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-100', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lst</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-101" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-101', 'list', 'link-101');">list</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-string">"join.english"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-102" class="py-name" targets="Function Bio.Decode.join_english()=Bio.Decode-module.html#join_english"><a title="Bio.Decode.join_english" class="py-name" href="#" onclick="return doclink('link-102', 'join_english', 'link-102');">join_english</a></tt><tt class="py-op">,</tt> <tt id="link-103" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-103', 'list', 'link-101');">list</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># Integer operations</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-string">"int"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-104" class="py-name" targets="Function Bio.Decode.safe_int()=Bio.Decode-module.html#safe_int"><a title="Bio.Decode.safe_int" class="py-name" href="#" onclick="return doclink('link-104', 'safe_int', 'link-104');">safe_int</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">"int.comma"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-105" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-105', 's', 'link-6');">s</a></tt><tt class="py-op">:</tt> <tt id="link-106" class="py-name"><a title="Bio.Decode.safe_int" class="py-name" href="#" onclick="return doclink('link-106', 'safe_int', 'link-104');">safe_int</a></tt><tt class="py-op">(</tt><tt id="link-107" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-107', 's', 'link-6');">s</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">","</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-string">"hex"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-name">hex</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-string">"oct"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-name">oct</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-string">"add"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-108" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-108', 'i', 'link-5');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">j</tt><tt class="py-op">:</tt> <tt id="link-109" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-109', 'i', 'link-5');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">j</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-comment"># Float operations</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-string">"float"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="_fixup_defs"></a><div id="_fixup_defs-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="_fixup_defs-toggle" onclick="return toggle('_fixup_defs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#_fixup_defs">_fixup_defs</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_fixup_defs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_fixup_defs-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-comment"># Normalize so the 2nd and 3rd terms are tuples</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-110" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-110', 'v', 'link-110');">v</a></tt> <tt class="py-keyword">in</tt> <tt id="link-111" class="py-name"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-111', 'decode_functions', 'link-69');">decode_functions</a></tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-112', 'items', 'link-112');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt class="py-name">out_types</tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-113', 'v', 'link-110');">v</a></tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt id="link-114" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-114', 'type', 'link-114');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">in_types</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">in_types</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt id="link-115" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-115', 'type', 'link-114');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">in_types</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">in_types</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">out_types</tt><tt class="py-op">,</tt> <tt id="link-116" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-116', 'type', 'link-114');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">out_types</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">out_types</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">out_types</tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-117', 'type', 'link-114');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">out_types</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">out_types</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt id="link-118" class="py-name"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-118', 'decode_functions', 'link-69');">decode_functions</a></tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt class="py-name">out_types</tt><tt class="py-op">)</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt id="link-119" class="py-name" targets="Function Bio.Decode._fixup_defs()=Bio.Decode-module.html#_fixup_defs"><a title="Bio.Decode._fixup_defs" class="py-name" href="#" onclick="return doclink('link-119', '_fixup_defs', 'link-119');">_fixup_defs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="Token"></a><div id="Token-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="Token-toggle" onclick="return toggle('Token');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Decode.Token-class.html">Token</a><tt class="py-op">:</tt> </tt>
</div><div id="Token-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Token-expanded"><a name="Token.__init__"></a><div id="Token.__init__-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="Token.__init__-toggle" onclick="return toggle('Token.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.Token-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">type</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Token.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Token.__init__-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-120', 'type', 'link-114');">type</a></tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-121', 'type', 'link-114');">type</a></tt> </tt>
</div><a name="Token.__cmp__"></a><div id="Token.__cmp__-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="Token.__cmp__-toggle" onclick="return toggle('Token.__cmp__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.Token-class.html#__cmp__">__cmp__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Token.__cmp__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Token.__cmp__-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-122', 'type', 'link-114');">type</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
</div><a name="Token.__repr__"></a><div id="Token.__repr__-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="Token.__repr__-toggle" onclick="return toggle('Token.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.Token-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Token.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Token.__repr__-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"Token(%r)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-123', 'type', 'link-114');">type</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="ValueToken"></a><div id="ValueToken-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="ValueToken-toggle" onclick="return toggle('ValueToken');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Decode.ValueToken-class.html">ValueToken</a><tt class="py-op">(</tt><tt class="py-base-class">Token</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ValueToken-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ValueToken-expanded"><a name="ValueToken.__init__"></a><div id="ValueToken.__init__-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="ValueToken.__init__-toggle" onclick="return toggle('ValueToken.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.ValueToken-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">type</tt><tt class="py-op">,</tt> <tt class="py-param">val</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ValueToken.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ValueToken.__init__-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt id="link-124" class="py-name" targets="Class Bio.Decode.Token=Bio.Decode.Token-class.html,Class Bio.GenBank.LocationParser.Token=Bio.GenBank.LocationParser.Token-class.html,Class Bio.LocusLink.web_parse.Token=Bio.LocusLink.web_parse.Token-class.html"><a title="Bio.Decode.Token
Bio.GenBank.LocationParser.Token
Bio.LocusLink.web_parse.Token" class="py-name" href="#" onclick="return doclink('link-124', 'Token', 'link-124');">Token</a></tt><tt class="py-op">.</tt><tt id="link-125" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method 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Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
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Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
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Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
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Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
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Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-137', '__init__', 'link-125');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.tokenize"></a><div id="DecodeScanner.tokenize-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="DecodeScanner.tokenize-toggle" onclick="return toggle('DecodeScanner.tokenize');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#tokenize">tokenize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.tokenize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.tokenize-expanded"><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-138" class="py-name"><a title="Bio.Parsers.spark.GenericScanner" class="py-name" href="#" onclick="return doclink('link-138', 'GenericScanner', 'link-3');">GenericScanner</a></tt><tt class="py-op">.</tt><tt id="link-139" class="py-name" targets="Method Bio.Decode.DecodeScanner.tokenize()=Bio.Decode.DecodeScanner-class.html#tokenize,Method Bio.GenBank.LocationParser.LocationScanner.tokenize()=Bio.GenBank.LocationParser.LocationScanner-class.html#tokenize,Method Bio.Parsers.spark.GenericScanner.tokenize()=Bio.Parsers.spark.GenericScanner-class.html#tokenize"><a title="Bio.Decode.DecodeScanner.tokenize
Bio.GenBank.LocationParser.LocationScanner.tokenize
Bio.Parsers.spark.GenericScanner.tokenize" class="py-name" href="#" onclick="return doclink('link-139', 'tokenize', 'link-139');">tokenize</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">input</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt> </tt>
</div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_functionname"></a><div id="DecodeScanner.t_functionname-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_functionname-toggle" onclick="return toggle('DecodeScanner.t_functionname');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_functionname">t_functionname</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_functionname-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_functionname-expanded"><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-docstring">r" \w+(\.\w+)*"</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-140', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-141" class="py-name" targets="Class Bio.Decode.FunctionName=Bio.Decode.FunctionName-class.html"><a title="Bio.Decode.FunctionName" class="py-name" href="#" onclick="return doclink('link-141', 'FunctionName', 'link-141');">FunctionName</a></tt><tt class="py-op">(</tt><tt class="py-name">input</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_pipe"></a><div id="DecodeScanner.t_pipe-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_pipe-toggle" onclick="return toggle('DecodeScanner.t_pipe');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_pipe">t_pipe</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_pipe-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_pipe-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-docstring">r" \| "</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-142', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-143" class="py-name"><a title="Bio.Decode.Token
Bio.GenBank.LocationParser.Token
Bio.LocusLink.web_parse.Token" class="py-name" href="#" onclick="return doclink('link-143', 'Token', 'link-124');">Token</a></tt><tt class="py-op">(</tt><tt class="py-string">"pipe"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_open_paren"></a><div id="DecodeScanner.t_open_paren-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_open_paren-toggle" onclick="return toggle('DecodeScanner.t_open_paren');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_open_paren">t_open_paren</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_open_paren-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_open_paren-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-docstring">r" \( "</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-144', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-145" class="py-name"><a title="Bio.Decode.Token
Bio.GenBank.LocationParser.Token
Bio.LocusLink.web_parse.Token" class="py-name" href="#" onclick="return doclink('link-145', 'Token', 'link-124');">Token</a></tt><tt class="py-op">(</tt><tt class="py-string">"open_paren"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_close_paren"></a><div id="DecodeScanner.t_close_paren-def"><a name="L190"></a><tt class="py-lineno">190</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_close_paren-toggle" onclick="return toggle('DecodeScanner.t_close_paren');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_close_paren">t_close_paren</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_close_paren-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_close_paren-expanded"><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-docstring">r" \) "</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-146', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-147" class="py-name"><a title="Bio.Decode.Token
Bio.GenBank.LocationParser.Token
Bio.LocusLink.web_parse.Token" class="py-name" href="#" onclick="return doclink('link-147', 'Token', 'link-124');">Token</a></tt><tt class="py-op">(</tt><tt class="py-string">"close_paren"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_comma"></a><div id="DecodeScanner.t_comma-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_comma-toggle" onclick="return toggle('DecodeScanner.t_comma');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_comma">t_comma</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_comma-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_comma-expanded"><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-docstring">r" , "</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-148', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Decode.Token
Bio.GenBank.LocationParser.Token
Bio.LocusLink.web_parse.Token" class="py-name" href="#" onclick="return doclink('link-149', 'Token', 'link-124');">Token</a></tt><tt class="py-op">(</tt><tt class="py-string">"comma"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_whitespace"></a><div id="DecodeScanner.t_whitespace-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_whitespace-toggle" onclick="return toggle('DecodeScanner.t_whitespace');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_whitespace">t_whitespace</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_whitespace-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_whitespace-expanded"><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-docstring">r" \s+ "</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_string"></a><div id="DecodeScanner.t_string-def"><a name="L202"></a><tt class="py-lineno">202</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_string-toggle" onclick="return toggle('DecodeScanner.t_string');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_string">t_string</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_string-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_string-expanded"><a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-docstring">r""" "([^"\\]+|\\.)*"|'([^'\\]+|\\.)*' """</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-comment"># "' # emacs cruft</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-150" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-150', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">input</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-151', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-152" class="py-name"><a title="Bio.Decode.unescape_C" class="py-name" href="#" onclick="return doclink('link-152', 'unescape_C', 'link-92');">unescape_C</a></tt><tt class="py-op">(</tt><tt id="link-153" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-153', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-154', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-155" class="py-name" targets="Class Bio.Decode.String=Bio.Decode.String-class.html"><a title="Bio.Decode.String" class="py-name" href="#" onclick="return doclink('link-155', 'String', 'link-155');">String</a></tt><tt class="py-op">(</tt><tt id="link-156" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-156', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </tt>
<a name="DecodeScanner.t_float"></a><div id="DecodeScanner.t_float-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="DecodeScanner.t_float-toggle" onclick="return toggle('DecodeScanner.t_float');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeScanner-class.html#t_float">t_float</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeScanner.t_float-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeScanner.t_float-expanded"><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-docstring">r""" [+-]?((\d+(\.\d*)?)|\.\d+)([eE][+-]?[0-9]+)? """</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-comment"># See if this is an integer</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-157', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-158" class="py-name" targets="Class Bio.Decode.Integer=Bio.Decode.Integer-class.html,Class Bio.GenBank.LocationParser.Integer=Bio.GenBank.LocationParser.Integer-class.html,Function Martel.Integer()=Martel-module.html#Integer"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-158', 'Integer', 'link-158');">Integer</a></tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Bio.Decode.safe_int" class="py-name" href="#" onclick="return doclink('link-159', 'safe_int', 'link-104');">safe_int</a></tt><tt class="py-op">(</tt><tt class="py-name">input</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rv</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-160', 'append', 'link-9');">append</a></tt><tt class="py-op">(</tt><tt id="link-161" class="py-name" targets="Class Bio.Decode.Float=Bio.Decode.Float-class.html,Function Martel.Float()=Martel-module.html#Float"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-161', 'Float', 'link-161');">Float</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">input</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> </tt>
<a name="Function"></a><div id="Function-def"><a name="L218"></a><tt class="py-lineno">218</tt> <a class="py-toggle" href="#" id="Function-toggle" onclick="return toggle('Function');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Decode.Function-class.html">Function</a><tt class="py-op">:</tt> </tt>
</div><div id="Function-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Function-expanded"><a name="Function.__init__"></a><div id="Function.__init__-def"><a name="L219"></a><tt class="py-lineno">219</tt> <a class="py-toggle" href="#" id="Function.__init__-toggle" onclick="return toggle('Function.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.Function-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Function.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Function.__init__-expanded"><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-162', 'name', 'link-162');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-163', 'name', 'link-162');">name</a></tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt> </tt>
</div><a name="Function.__str__"></a><div id="Function.__str__-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="Function.__str__-toggle" onclick="return toggle('Function.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.Function-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Function.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Function.__str__-expanded"><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt id="link-164" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-164', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt id="link-165" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-165', 's', 'link-6');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s(x, %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-166', 'name', 'link-162');">name</a></tt><tt class="py-op">,</tt> <tt id="link-167" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-167', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt id="link-168" class="py-name" targets="Method Bio.Align.Generic.Alignment.__repr__()=Bio.Align.Generic.Alignment-class.html#__repr__,Method Bio.Alphabet.Alphabet.__repr__()=Bio.Alphabet.Alphabet-class.html#__repr__,Method Bio.Alphabet.AlphabetEncoder.__repr__()=Bio.Alphabet.AlphabetEncoder-class.html#__repr__,Method Bio.Crystal.Crystal.__repr__()=Bio.Crystal.Crystal-class.html#__repr__,Method Bio.Crystal.Hetero.__repr__()=Bio.Crystal.Hetero-class.html#__repr__,Method Bio.Decode.Token.__repr__()=Bio.Decode.Token-class.html#__repr__,Method Bio.Decode.ValueToken.__repr__()=Bio.Decode.ValueToken-class.html#__repr__,Method Bio.DocSQL.Query.__repr__()=Bio.DocSQL.Query-class.html#__repr__,Method Bio.EUtils.Datatypes.CheckLinkSet.__repr__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__repr__,Method Bio.EUtils.Datatypes.DBIds.__repr__()=Bio.EUtils.Datatypes.DBIds-class.html#__repr__,Method Bio.EUtils.Datatypes.Date.__repr__()=Bio.EUtils.Datatypes.Date-class.html#__repr__,Method Bio.EUtils.Datatypes.EUtilsSearchError.__repr__()=Bio.EUtils.Datatypes.EUtilsSearchError-class.html#__repr__,Method Bio.EUtils.Datatypes.IdCheck.__repr__()=Bio.EUtils.Datatypes.IdCheck-class.html#__repr__,Method Bio.EUtils.Datatypes.IdUrlSet.__repr__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__repr__,Method Bio.EUtils.Datatypes.Link.__repr__()=Bio.EUtils.Datatypes.Link-class.html#__repr__,Method Bio.EUtils.Datatypes.LinkSetDb.__repr__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__repr__,Method Bio.EUtils.Datatypes.LinksLinkSet.__repr__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__repr__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__repr__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__repr__,Method Bio.EUtils.Datatypes.ObjUrl.__repr__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__repr__,Method Bio.EUtils.Datatypes.Problem.__repr__()=Bio.EUtils.Datatypes.Problem-class.html#__repr__,Method Bio.EUtils.Datatypes.Provider.__repr__()=Bio.EUtils.Datatypes.Provider-class.html#__repr__,Method Bio.EUtils.Datatypes.Summary.__repr__()=Bio.EUtils.Datatypes.Summary-class.html#__repr__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__repr__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__repr__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__repr__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__repr__,Method Bio.EUtils.POM.AttributeList.__repr__()=Bio.EUtils.POM.AttributeList-class.html#__repr__,Method Bio.EUtils.POM.ContentModel.__repr__()=Bio.EUtils.POM.ContentModel-class.html#__repr__,Method Bio.EUtils.POM.ElementNode.__repr__()=Bio.EUtils.POM.ElementNode-class.html#__repr__,Method Bio.EUtils.POM.IndentedText.__repr__()=Bio.EUtils.POM.IndentedText-class.html#__repr__,Method Bio.EUtils.POM.XMLAttribute.__repr__()=Bio.EUtils.POM.XMLAttribute-class.html#__repr__,Method Bio.EUtils.POM._AttributeType.__repr__()=Bio.EUtils.POM._AttributeType-class.html#__repr__,Method Bio.EUtils.POM._ContentModelGenerator.__repr__()=Bio.EUtils.POM._ContentModelGenerator-class.html#__repr__,Method Bio.Enzyme.EnzymeRecord.__repr__()=Bio.Enzyme.EnzymeRecord-class.html#__repr__,Method Bio.FSSP.FSSPSumRec.__repr__()=Bio.FSSP.FSSPSumRec-class.html#__repr__,Method Bio.FSSP.PosAlign.__repr__()=Bio.FSSP.PosAlign-class.html#__repr__,Method Bio.FSSP.fssp_rec.fff_rec.__repr__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__repr__,Method Bio.GFF.easy.Location.__repr__()=Bio.GFF.easy.Location-class.html#__repr__,Method Bio.GenBank.LocationParser.AbsoluteLocation.__repr__()=Bio.GenBank.LocationParser.AbsoluteLocation-class.html#__repr__,Method Bio.GenBank.LocationParser.Between.__repr__()=Bio.GenBank.LocationParser.Between-class.html#__repr__,Method Bio.GenBank.LocationParser.FeatureName.__repr__()=Bio.GenBank.LocationParser.FeatureName-class.html#__repr__,Method Bio.GenBank.LocationParser.Function.__repr__()=Bio.GenBank.LocationParser.Function-class.html#__repr__,Method 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Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-171', '__init__', 'link-125');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-172" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-172', 'start', 'link-172');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">begin_pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> </tt>
<a name="DecodeParser.p_expression"></a><div id="DecodeParser.p_expression-def"><a name="L236"></a><tt class="py-lineno">236</tt> <a class="py-toggle" href="#" id="DecodeParser.p_expression-toggle" onclick="return toggle('DecodeParser.p_expression');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeParser-class.html#p_expression">p_expression</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeParser.p_expression-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeParser.p_expression-expanded"><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> expression ::= term</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> expression ::= term pipe expression</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="DecodeParser.p_term"></a><div id="DecodeParser.p_term-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="DecodeParser.p_term-toggle" onclick="return toggle('DecodeParser.p_term');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeParser-class.html#p_term">p_term</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeParser.p_term-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeParser.p_term-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> term ::= functionname</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> term ::= functionname open_paren args close_paren</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-173" class="py-name" targets="Class Bio.Decode.Function=Bio.Decode.Function-class.html,Class Bio.GenBank.LocationParser.Function=Bio.GenBank.LocationParser.Function-class.html"><a title="Bio.Decode.Function
Bio.GenBank.LocationParser.Function" class="py-name" href="#" onclick="return doclink('link-173', 'Function', 'link-173');">Function</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-174" class="py-name"><a title="Bio.Decode.Function
Bio.GenBank.LocationParser.Function" class="py-name" href="#" onclick="return doclink('link-174', 'Function', 'link-173');">Function</a></tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-175" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-175', 'x', 'link-15');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">val</tt> <tt class="py-keyword">for</tt> <tt id="link-176" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-176', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="DecodeParser.p_args"></a><div id="DecodeParser.p_args-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="DecodeParser.p_args-toggle" onclick="return toggle('DecodeParser.p_args');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeParser-class.html#p_args">p_args</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeParser.p_args-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeParser.p_args-expanded"><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-docstring"> args ::= arg</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> args ::= arg comma args</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="DecodeParser.p_arg"></a><div id="DecodeParser.p_arg-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="DecodeParser.p_arg-toggle" onclick="return toggle('DecodeParser.p_arg');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.DecodeParser-class.html#p_arg">p_arg</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DecodeParser.p_arg-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DecodeParser.p_arg-expanded"><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> arg ::= string</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> arg ::= integer</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> arg ::= float</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="scan"></a><div id="scan-def"><a name="L271"></a><tt class="py-lineno">271</tt> <a class="py-toggle" href="#" id="scan-toggle" onclick="return toggle('scan');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#scan">scan</a><tt class="py-op">(</tt><tt class="py-param">input</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="scan-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="scan-expanded"><a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">scanner</tt> <tt class="py-op">=</tt> <tt id="link-177" class="py-name" targets="Class Bio.Decode.DecodeScanner=Bio.Decode.DecodeScanner-class.html"><a title="Bio.Decode.DecodeScanner" class="py-name" href="#" onclick="return doclink('link-177', 'DecodeScanner', 'link-177');">DecodeScanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">scanner</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.Decode.DecodeScanner.tokenize
Bio.GenBank.LocationParser.LocationScanner.tokenize
Bio.Parsers.spark.GenericScanner.tokenize" class="py-name" href="#" onclick="return doclink('link-178', 'tokenize', 'link-139');">tokenize</a></tt><tt class="py-op">(</tt><tt class="py-name">input</tt><tt class="py-op">)</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">tokens</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-179" class="py-name" targets="Class Bio.Decode.DecodeParser=Bio.Decode.DecodeParser-class.html"><a title="Bio.Decode.DecodeParser" class="py-name" href="#" onclick="return doclink('link-179', 'DecodeParser', 'link-179');">DecodeParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-180" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-180', 'parse', 'link-180');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">tokens</tt><tt class="py-op">)</tt> </tt>
</div><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt id="link-181" class="py-name" targets="Variable Bio.Decode._decoder_cache=Bio.Decode-module.html#_decoder_cache"><a title="Bio.Decode._decoder_cache" class="py-name" href="#" onclick="return doclink('link-181', '_decoder_cache', 'link-181');">_decoder_cache</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="FunctionCall"></a><div id="FunctionCall-def"><a name="L281"></a><tt class="py-lineno">281</tt> <a class="py-toggle" href="#" id="FunctionCall-toggle" onclick="return toggle('FunctionCall');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Decode.FunctionCall-class.html">FunctionCall</a><tt class="py-op">:</tt> </tt>
</div><div id="FunctionCall-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FunctionCall-expanded"><a name="FunctionCall.__init__"></a><div id="FunctionCall.__init__-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="FunctionCall.__init__-toggle" onclick="return toggle('FunctionCall.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.FunctionCall-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">f</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionCall.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FunctionCall.__init__-expanded"><a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt> </tt>
</div><a name="FunctionCall.__call__"></a><div id="FunctionCall.__call__-def"><a name="L285"></a><tt class="py-lineno">285</tt> <a class="py-toggle" href="#" id="FunctionCall.__call__-toggle" onclick="return toggle('FunctionCall.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.FunctionCall-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionCall.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FunctionCall.__call__-expanded"><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">f</tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-182', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="FunctionCallChain"></a><div id="FunctionCallChain-def"><a name="L288"></a><tt class="py-lineno">288</tt> <a class="py-toggle" href="#" id="FunctionCallChain-toggle" onclick="return toggle('FunctionCallChain');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Decode.FunctionCallChain-class.html">FunctionCallChain</a><tt class="py-op">:</tt> </tt>
</div><div id="FunctionCallChain-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FunctionCallChain-expanded"><a name="FunctionCallChain.__init__"></a><div id="FunctionCallChain.__init__-def"><a name="L289"></a><tt class="py-lineno">289</tt> <a class="py-toggle" href="#" id="FunctionCallChain.__init__-toggle" onclick="return toggle('FunctionCallChain.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.FunctionCallChain-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">inner_f</tt><tt class="py-op">,</tt> <tt class="py-param">f</tt><tt class="py-op">,</tt> <tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionCallChain.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FunctionCallChain.__init__-expanded"><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inner_f</tt> <tt class="py-op">=</tt> <tt class="py-name">inner_f</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt> </tt>
</div><a name="FunctionCallChain.__call__"></a><div id="FunctionCallChain.__call__-def"><a name="L293"></a><tt class="py-lineno">293</tt> <a class="py-toggle" href="#" id="FunctionCallChain.__call__-toggle" onclick="return toggle('FunctionCallChain.__call__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode.FunctionCallChain-class.html#__call__">__call__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FunctionCallChain.__call__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FunctionCallChain.__call__-expanded"><a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">f</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">inner_f</tt><tt class="py-op">(</tt><tt id="link-183" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-183', 'x', 'link-15');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-comment">#### I don't think this is the right way to do things</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##class CheckTypes:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## def __init__(self, f, call_types, return_types):</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.f = f</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.call_types = call_types</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.return_types = return_types</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## def __call__(self, x):</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if self.call_types is not None:</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## for T in self.call_types:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if isinstance(x, T):</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## break</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## raise TypeError(</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## "Call value %s of type %s, expecting one of %s" %</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## (x, type(x).__name__,</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## [T.name for T in self.call_types]))</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## y = self.f(x)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-comment">## if not self.return_types:</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## return y</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment">## for T in self.return_types:</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if isinstance(y, T):</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## return y</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## raise TypeError("Return value %s of type %s, expecting one of %s" %</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## (y, type(y).__name__,</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## [T.name for T in self.return_types]))</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="make_decoder"></a><div id="make_decoder-def"><a name="L324"></a><tt class="py-lineno">324</tt> <a class="py-toggle" href="#" id="make_decoder-toggle" onclick="return toggle('make_decoder');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#make_decoder">make_decoder</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="make_decoder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_decoder-expanded"><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-184" class="py-name"><a title="Bio.Decode._decoder_cache" class="py-name" href="#" onclick="return doclink('link-184', '_decoder_cache', 'link-181');">_decoder_cache</a></tt><tt class="py-op">[</tt><tt id="link-185" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-185', 's', 'link-6');">s</a></tt><tt class="py-op">]</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">functions</tt> <tt class="py-op">=</tt> <tt id="link-186" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-186', 'parse', 'link-180');">parse</a></tt><tt class="py-op">(</tt><tt id="link-187" class="py-name" targets="Function Bio.Decode.scan()=Bio.Decode-module.html#scan,Function Bio.GenBank.LocationParser.scan()=Bio.GenBank.LocationParser-module.html#scan"><a title="Bio.Decode.scan
Bio.GenBank.LocationParser.scan" class="py-name" href="#" onclick="return doclink('link-187', 'scan', 'link-187');">scan</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-188', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">functions</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">fc</tt> <tt class="py-op">=</tt> <tt id="link-189" class="py-name"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-189', 'decode_functions', 'link-69');">decode_functions</a></tt><tt class="py-op">[</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-190', 'name', 'link-162');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">fc</tt> <tt class="py-op">=</tt> <tt id="link-191" class="py-name" targets="Class Bio.Decode.FunctionCall=Bio.Decode.FunctionCall-class.html"><a title="Bio.Decode.FunctionCall" class="py-name" href="#" onclick="return doclink('link-191', 'FunctionCall', 'link-191');">FunctionCall</a></tt><tt class="py-op">(</tt><tt class="py-name">fc</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">functions</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">fc</tt> <tt class="py-op">=</tt> <tt id="link-192" class="py-name" targets="Class Bio.Decode.FunctionCallChain=Bio.Decode.FunctionCallChain-class.html"><a title="Bio.Decode.FunctionCallChain" class="py-name" href="#" onclick="return doclink('link-192', 'FunctionCallChain', 'link-192');">FunctionCallChain</a></tt><tt class="py-op">(</tt><tt class="py-name">fc</tt><tt class="py-op">,</tt> <tt id="link-193" class="py-name"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-193', 'decode_functions', 'link-69');">decode_functions</a></tt><tt class="py-op">[</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-194', 'name', 'link-162');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt id="link-195" class="py-name"><a title="Bio.Decode._decoder_cache" class="py-name" href="#" onclick="return doclink('link-195', '_decoder_cache', 'link-181');">_decoder_cache</a></tt><tt class="py-op">[</tt><tt id="link-196" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-196', 's', 'link-6');">s</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">fc</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fc</tt> </tt>
</div><a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> </tt>
<a name="_verify_subtypes"></a><div id="_verify_subtypes-def"><a name="L342"></a><tt class="py-lineno">342</tt> <a class="py-toggle" href="#" id="_verify_subtypes-toggle" onclick="return toggle('_verify_subtypes');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#_verify_subtypes">_verify_subtypes</a><tt class="py-op">(</tt><tt class="py-param">subset</tt><tt class="py-op">,</tt> <tt class="py-param">total</tt><tt class="py-op">,</tt> <tt class="py-param">old_name</tt><tt class="py-op">,</tt> <tt class="py-param">new_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_verify_subtypes-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_verify_subtypes-expanded"><a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-197" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-197', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">subset</tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-198" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-198', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">total</tt><tt class="py-op">:</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"%s can produce a %r value not accepted by %s"</tt> <tt class="py-op">%</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">old_name</tt><tt class="py-op">,</tt> <tt id="link-199" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-199', 'x', 'link-15');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> <tt class="py-name">new_name</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt id="link-200" class="py-name" targets="Variable Bio.Decode._typechecked_decoder_cache=Bio.Decode-module.html#_typechecked_decoder_cache"><a title="Bio.Decode._typechecked_decoder_cache" class="py-name" href="#" onclick="return doclink('link-200', '_typechecked_decoder_cache', 'link-200');">_typechecked_decoder_cache</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="make_typechecked_decoder"></a><div id="make_typechecked_decoder-def"><a name="L349"></a><tt class="py-lineno">349</tt> <a class="py-toggle" href="#" id="make_typechecked_decoder-toggle" onclick="return toggle('make_typechecked_decoder');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#make_typechecked_decoder">make_typechecked_decoder</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">input_types</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">output_types</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="make_typechecked_decoder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_typechecked_decoder-expanded"><a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">cache_lookup</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-201" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-201', 's', 'link-6');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">input_types</tt><tt class="py-op">,</tt> <tt class="py-name">output_types</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-202" class="py-name"><a title="Bio.Decode._typechecked_decoder_cache" class="py-name" href="#" onclick="return doclink('link-202', '_typechecked_decoder_cache', 'link-200');">_typechecked_decoder_cache</a></tt><tt class="py-op">[</tt><tt class="py-name">cache_lookup</tt><tt class="py-op">]</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">input_types</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">input_types</tt><tt class="py-op">,</tt> <tt id="link-203" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-203', 'type', 'link-114');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-name">input_types</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">input_types</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">output_types</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">output_types</tt><tt class="py-op">,</tt> <tt id="link-204" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-204', 'type', 'link-114');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">output_types</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">output_types</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">functions</tt> <tt class="py-op">=</tt> <tt id="link-205" class="py-name"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-205', 'parse', 'link-180');">parse</a></tt><tt class="py-op">(</tt><tt id="link-206" class="py-name"><a title="Bio.Decode.scan
Bio.GenBank.LocationParser.scan" class="py-name" href="#" onclick="return doclink('link-206', 'scan', 'link-187');">scan</a></tt><tt class="py-op">(</tt><tt id="link-207" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-207', 's', 'link-6');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-comment"># Make sure the input type(s) are allowed</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">functions</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">fc</tt><tt class="py-op">,</tt> <tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt class="py-name">out_types</tt> <tt class="py-op">=</tt> <tt id="link-208" class="py-name"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-208', 'decode_functions', 'link-69');">decode_functions</a></tt><tt class="py-op">[</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-209', 'name', 'link-162');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">input_types</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-210" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-210', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">input_types</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-211" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-211', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">in_types</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-string">"the input type includes %r which isn't supported by %s"</tt> <tt class="py-op">%</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-212" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-212', 'x', 'link-15');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-213', 'name', 'link-162');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-comment"># Do the composition</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">old_name</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-214', 'name', 'link-162');">name</a></tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-name">input_types</tt> <tt class="py-op">=</tt> <tt class="py-name">out_types</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">functions</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">fc</tt> <tt class="py-op">=</tt> <tt id="link-215" class="py-name"><a title="Bio.Decode.FunctionCall" class="py-name" href="#" onclick="return doclink('link-215', 'FunctionCall', 'link-191');">FunctionCall</a></tt><tt class="py-op">(</tt><tt class="py-name">fc</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">functions</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">transform_func</tt><tt class="py-op">,</tt> <tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt class="py-name">out_types</tt> <tt class="py-op">=</tt> <tt id="link-216" class="py-name"><a title="Bio.Decode.decode_functions" class="py-name" href="#" onclick="return doclink('link-216', 'decode_functions', 'link-69');">decode_functions</a></tt><tt class="py-op">[</tt><tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-217', 'name', 'link-162');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt id="link-218" class="py-name" targets="Function Bio.Decode._verify_subtypes()=Bio.Decode-module.html#_verify_subtypes"><a title="Bio.Decode._verify_subtypes" class="py-name" href="#" onclick="return doclink('link-218', '_verify_subtypes', 'link-218');">_verify_subtypes</a></tt><tt class="py-op">(</tt><tt class="py-name">input_types</tt><tt class="py-op">,</tt> <tt class="py-name">in_types</tt><tt class="py-op">,</tt> <tt class="py-name">old_name</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-219', 'name', 'link-162');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">old_name</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-220', 'name', 'link-162');">name</a></tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">input_types</tt> <tt class="py-op">=</tt> <tt class="py-name">out_types</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">fc</tt> <tt class="py-op">=</tt> <tt id="link-221" class="py-name"><a title="Bio.Decode.FunctionCallChain" class="py-name" href="#" onclick="return doclink('link-221', 'FunctionCallChain', 'link-192');">FunctionCallChain</a></tt><tt class="py-op">(</tt><tt class="py-name">fc</tt><tt class="py-op">,</tt> <tt class="py-name">transform_func</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">output_types</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt id="link-222" class="py-name"><a title="Bio.Decode._verify_subtypes" class="py-name" href="#" onclick="return doclink('link-222', '_verify_subtypes', 'link-218');">_verify_subtypes</a></tt><tt class="py-op">(</tt><tt class="py-name">input_types</tt><tt class="py-op">,</tt> <tt class="py-name">output_types</tt><tt class="py-op">,</tt> <tt class="py-name">old_name</tt><tt class="py-op">,</tt> <tt class="py-string">"the output"</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt id="link-223" class="py-name"><a title="Bio.Decode._typechecked_decoder_cache" class="py-name" href="#" onclick="return doclink('link-223', '_typechecked_decoder_cache', 'link-200');">_typechecked_decoder_cache</a></tt><tt class="py-op">[</tt><tt class="py-name">cache_lookup</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">fc</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fc</tt> </tt>
</div><a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> </tt>
<a name="test"></a><div id="test-def"><a name="L392"></a><tt class="py-lineno">392</tt> <a class="py-toggle" href="#" id="test-toggle" onclick="return toggle('test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Decode-module.html#test">test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="test-expanded"><a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-224" class="py-name" targets="Function Bio.Decode.make_decoder()=Bio.Decode-module.html#make_decoder"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-224', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">"chop"</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"Andrew"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"Andre"</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-225" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-225', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">"int"</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"9"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">9</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-226" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-226', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'join(" ")'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"Andrew"</tt><tt class="py-op">,</tt> <tt class="py-string">"Dalke"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> \ </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-string">"Andrew Dalke"</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-227" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-227', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'chomp("|")'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"|test|"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"|test"</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-228" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-228', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'chomp("|")'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"|test"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"|test"</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-229" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-229', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'chomp("A")|chop'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"BA"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-230" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-230', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'chomp("A")|chop'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"AB"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"A"</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-231" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-231', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'chop|chomp("A")'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"AB"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-232" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-232', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'chop|chomp("A")'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-string">"BA"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"B"</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-233" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-233', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'add(5)'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">7</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-234" class="py-name"><a title="Bio.Decode.make_decoder" class="py-name" href="#" onclick="return doclink('link-234', 'make_decoder', 'link-224');">make_decoder</a></tt><tt class="py-op">(</tt><tt class="py-string">'add(-2)'</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt> </tt>
</div><a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt id="link-235" class="py-name" targets="Function Bio.Decode.test()=Bio.Decode-module.html#test,Function Bio.EUtils.ReseekFile.test()=Bio.EUtils.ReseekFile-module.html#test,Package Martel.test=Martel.test-module.html,Method Martel.test.support.Storage.test()=Martel.test.support.Storage-class.html#test,Function Martel.test.test()=Martel.test-module.html#test,Function Martel.test.test_Expression.test()=Martel.test.test_Expression-module.html#test,Function Martel.test.test_Generate.test()=Martel.test.test_Generate-module.html#test,Function Martel.test.test_IterParser.test()=Martel.test.test_IterParser-module.html#test,Function Martel.test.test_Iterator.test()=Martel.test.test_Iterator-module.html#test,Function Martel.test.test_LAX.test()=Martel.test.test_LAX-module.html#test,Function Martel.test.test_ParseRecords.test()=Martel.test.test_ParseRecords-module.html#test,Function Martel.test.test_Parser.test()=Martel.test.test_Parser-module.html#test,Function Martel.test.test_RecordReader.test()=Martel.test.test_RecordReader-module.html#test,Function Martel.test.test_RecordReader2.test()=Martel.test.test_RecordReader2-module.html#test,Function Martel.test.test_Time.test()=Martel.test.test_Time-module.html#test,Function Martel.test.test_attrs.test()=Martel.test.test_attrs-module.html#test,Function Martel.test.test_convert_re.test()=Martel.test.test_convert_re-module.html#test,Function Martel.test.test_delimiter.test()=Martel.test.test_delimiter-module.html#test,Function Martel.test.test_macros.test()=Martel.test.test_macros-module.html#test,Function Martel.test.test_optimize.test()=Martel.test.test_optimize-module.html#test,Function Martel.test.test_swissprot38.test()=Martel.test.test_swissprot38-module.html#test"><a title="Bio.Decode.test
Bio.EUtils.ReseekFile.test
Martel.test
Martel.test.support.Storage.test
Martel.test.test
Martel.test.test_Expression.test
Martel.test.test_Generate.test
Martel.test.test_IterParser.test
Martel.test.test_Iterator.test
Martel.test.test_LAX.test
Martel.test.test_ParseRecords.test
Martel.test.test_Parser.test
Martel.test.test_RecordReader.test
Martel.test.test_RecordReader2.test
Martel.test.test_Time.test
Martel.test.test_attrs.test
Martel.test.test_convert_re.test
Martel.test.test_delimiter.test
Martel.test.test_macros.test
Martel.test.test_optimize.test
Martel.test.test_swissprot38.test" class="py-name" href="#" onclick="return doclink('link-235', 'test', 'link-235');">test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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